Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Brd4

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver_ChIPSeq_Brd4_LapTTA_WT
strain background
C57BL/6
genotype/variation
WT
tissue
Liver
chip antibody
BRD4 (Bethyl, A301-985A100)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, HNF4a, BRD4, Histone Marks, RNAPol2 ChIP dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate) and 1% formaldehyde (FA). For ATAC seq experiments, 100,000 cells obtained from liver perfused mice were lysed to obtain nuclei. Transposition reaction and DNA purification were then performed. For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. For ATAC seq, libraries were prepared for Illumina sequencing with index primers.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
36726197
Reads aligned (%)
79.4
Duplicates removed (%)
18.0
Number of peaks
11657 (qval < 1E-05)

mm9

Number of total reads
36726197
Reads aligned (%)
79.1
Duplicates removed (%)
18.0
Number of peaks
11638 (qval < 1E-05)

Base call quality data from DBCLS SRA